You might have a situation here where there were several halfcrown dies used over time for the proofs from the sets. We already have an 1839, 1839/41 & 1839/43 halfpenny plus an 1839 sixpence with both the first and third head obverse, not to mention any number of Una varieties. The sixpences provided anecdotal evidence of the 1839 sets being produced up to the 1880s, given the third head was only introduced in 1880 - otherwise it is difficult to come up with a logical reason for making one 40+ years after they were first issued. We do know that sets were produced to order after 1839.
I suspect ESC is incomplete in its designation of what was included in the sets, but haven't checked what is extant in complete sets as of today. There is an argument for saying the Unas were struck separately because people would likely have wanted one as a stand alone piece, but the same could not be said for the humble halfpenny which are only likely to have been made as part of a set, and here we know of at least three dies used. The halfcrown could also be a case of more than one die pair being used in the sets.
More research is definitely required.